header file restructuring

Move all protocol definitions to protocol/*.h and keep only
definitions related to our implementation as *.h in the top directory.

Also, remove some header files to reduce header file proliferation.
diff --git a/src/diag_io.c b/src/diag_io.c
index b8dd18b..f9abd87 100644
--- a/src/diag_io.c
+++ b/src/diag_io.c
@@ -5,7 +5,7 @@
 #include <string.h>
 #include <unistd.h>
 
-#include "protocol.h"
+#include "protocol/protocol.h"
 #include "diag_io.h"
 #include "diagchar_hdlc.h"